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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF RAT ACID PHOSPHATASE IN COMPLEX WITH L(+) TARTRATE
 
Authors :  Y. Lindqvist, G. Schneider
Date :  12 Jun 93  (Deposition) - 31 May 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase(Phosphoric Monoester) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Lindqvist, G. Schneider, P. Vihko
Three-Dimensional Structure Of Rat Acid Phosphatase In Complex With L(+)-Tartrate.
J. Biol. Chem. V. 268 20744 1993
PubMed-ID: 8407898
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROSTATIC ACID PHOSPHATASE
    ChainsA
    EC Number3.1.3.2
    EngineeredYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3TAR1Ligand/IonD(-)-TARTARIC ACID
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3TAR2Ligand/IonD(-)-TARTARIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:272 , LEU A:274 , ASN A:301 , GLU A:302 , TYR A:308 , NAG A:345BINDING SITE FOR RESIDUE NAG A 344
2AC2SOFTWARETYR A:308 , NAG A:344 , BMA A:346BINDING SITE FOR RESIDUE NAG A 345
3AC3SOFTWARENAG A:345BINDING SITE FOR RESIDUE BMA A 346
4AC4SOFTWAREASN A:62 , SER A:64 , LYS A:66BINDING SITE FOR RESIDUE NAG A 347
5AC5SOFTWAREARG A:11 , HIS A:12 , ARG A:15 , ILE A:18 , ARG A:79 , HIS A:257 , ASP A:258BINDING SITE FOR RESIDUE TAR A 343

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:129 -A:340
2A:315 -A:319

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:124 -Pro A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RPA)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIS_ACID_PHOSPHAT_1PS00616 Histidine acid phosphatases phosphohistidine signature.PPAP_RAT34-48  1A:3-17
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIS_ACID_PHOSPHAT_1PS00616 Histidine acid phosphatases phosphohistidine signature.PPAP_RAT34-48  2A:3-17

(-) Exons   (0, 0)

(no "Exon" information available for 1RPA)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:342
 aligned with PPAP_RAT | P20646 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:342
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371  
             PPAP_RAT    32 KELKFVTLVFRHGDRGPIETFPNDPIKESSWPQGFGQLTKWGMGQHYELGSYIRRRYGRFLNNSYKHDQVYIRSTDVDRTLMSAMTNLAALFPPEGISIWNPRLLWQPIPVHTVSLSEDRLLYLPFRDCPRFQELKSETLKSEEFLKRLQPYKSFIDTLPSLSGFEDQDLFEIWSRLYDPLYCESVHNFTFRTWATEDAMTKLKELSELSLLSLYGIHKQKEKSRLQGGVLVNEILKNMKLATQPQKARKLIMYSAYDTTVSGLQMALELYNGLLPPYASCHIMELYQDNGGTFVEMYYRNETQNEPYPLTLPGCTHSCPLEKFAELLDPVIPQDWATECMG 373
               SCOP domains d1rpaa_ A: Prostatic acid phosphatase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1rpaA00 A:1-342 Phosphoglycerate mutase-like                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -His_Phos_2-1rpaA01 A:2-300                                                                                                                                                                                                                                                                                 ------------------------------------------ Pfam domains
     Sec.struct. author (1) ..eeeeeeeee............................hhhhhhhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh....................eee...............hhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhh......hhhhhhh.hhhhhhhh...........hhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhh............eeeeeeeee..eeeeeeeee.......eee........--hhhhhhhh.......hhhh... Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eee--------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --HIS_ACID_PHOSPH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rpa A   1 KELKFVTLVFRHGDRGPIETFPNDPIKESSWPQGFGQLTKWGMGQHYELGSYIRRRYGRFLNNSYKHDQVYIRSTDVDRTLMSAMTNLAALFPPEGNSIWNPRLLWQPIPVHTVSLSEDRLLYLPFRDCPRFQELKSETLKSEEFLKRLQPYKSFIDTLPSLSGFEDQDLFEIWSRLYDPLYCESVHNFTLPTWATEDAMTKLKELSELSLLSLYGIHKQKEKSRLQGGVLVNEILKNMKLATQPQKARKLIMYSAHDTTVSGLQMALDVYNGLLPPYASCHIMELYQDNGGHFVEMYYRNETQNEPYPLTLPGCTHSCPLEKFAELLDPVIPQDWATECMG 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PGM (50)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (PPAP_RAT | P20646)
molecular function
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    GO:0033265    choline binding    Interacting selectively and non-covalently with choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0031985    Golgi cisterna    Any of the thin, flattened membrane-bounded compartments that form the central portion of the Golgi complex.
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005771    multivesicular body    A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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